I wouldn't give any of those milks from tetra packs you can buy in the shops. If you wanted to give milk I would make homemade almond milk or coconut milk. As for calcium I would get him onto bone broth and try and get him eating sardines and leafy greens.

Also, look into healing his gut so that he doesn't have food intolerances. Best to heal the cause than just treat the symptoms IMO.

We are doing GAPS to heal our guts, but we're currently off dairy too. My 17 month old was also reacting to it so I've cut it all out for now and we'll start a reintroduction after 6 weeks. As he's BFing I don't give him any other milks.